I just want to make a PDB file containing few water molecules to
insert into a nanotube. I tried it several ways.

Using molefracture facility, I tried

* Making a PDB for a single water molecule and used periodic facility
to align several water molecules in Z direction. But I couldn't get
this file save as PDB,
when I save it only one molecules is there.

* Then making single molecule PDB files and add them all using tcl
commands calling the psfgen.